Ribonucleic acid, or RNA, is one of the two types of nucleic acids found in life on Earth. The other, deoxyribonucleic acid (DNA), has long assumed a higher profile than RNA in popular culture, in the minds of casual observers and elsewhere. RNA, however, is the more versatile nucleic acid; it takes the instructions it receives from DNA and transforms them into a variety of coordinated activities involved in protein synthesis. Looked at in this way, DNA might be viewed as the president or chancellor whose input ultimately determines what happens at the level of everyday events, whereas RNA is the army of loyal foot soldiers and grunt workers who get the actual jobs done and display a wide range of impressive skills in the process.
Basic Structure of RNA
RNA, like DNA, is a macromolecule (in other words, a molecule with a relatively large number of individual atoms, unlike, say, CO2 or H2O) consisting of a polymer, or chain of repeating chemical elements. The "links" in this chain, or more formally the monomers that make up the polymer, are called nucleotides. A single nucleotide consists in turn of three distinct chemical regions, or moieties: a pentose sugar, a phosphate group and a nitrogenous base. The nitrogenous bases may be one of four different bases: adenine (A), cytosine (C), guanine (G) and uracil (U).
Adenine and guanine are chemically classified as purines, whereas cytosine and uracil belong to the category of substances called pyrimidines. Purines consist chiefly of a five-member ring joined to a six-member rings, while pyrimidines are considerably smaller and have only a six-carbon ring. Adenine and guanine are very similar in structure to each other, as are cytosine and uracil.
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The pentose sugar in RNA is ribose, which includes a ring with five carbon atoms and one oxygen atom. The phosphate group is bonded to a carbon atom in the ring on one side of the oxygen atom, and the nitrogenous base is bonded to the carbon atom on the other side of the oxygen. The phosphate group also binds to the ribose on the adjacent nucleotide, so the ribose and phosphate portion of a nucleotide together make up the "backbone" of RNA.
The nitrogenous bases may be regarded as the most critical part of RNA, because it is these, in groups of three in adjoining nucleotides, that are of utmost functional importance. Groups of three adjacent bases form units called triplet codes, or codons, that carry special signals to the machinery that puts proteins together using the information wired into first DNA and then RNA. Without this code being interpreted as it is, the order of nucleotides would be irrelevant, as will be described shortly.
Differences Between DNA and RNA
When people with a little background in biology hear the term "DNA," it is likely that one of the first things that comes to mind is the "double helix." The distinctive structure of the DNA molecule was elucidated by Watson, Crick, Franklin and others in 1953, and among the team's findings was that DNA is double-stranded, and helical, in its usual form. RNA, in contrast, is virtually always single-stranded.
Also, as the names of these respective macromolecules imply, DNA contains a different ribose sugar. Instead of ribose, it contains deoxyribose, a compound identical to ribose save for having a hydrogen atom in place of one of its hydroxyl (-OH) groups.
Finally, while the pyrimidines in RNA are cytosine and uracil, in DNA they are cytosine and thymine. In the "rungs" of the double-stranded DNA "ladder," adenine binds with and only with thymine, while cytosine binds with and only with guanine. (Can you think of an architectural reason that purine bases only bind to pyrimidine bases across the center of DNA? Hint: the "sides" of the ladder must remain a fixed distance apart.) When DNA is transcribed and a complementary strand of RNA is created, the nucleotide generated across from the adenine in DNA is uracil, not thymine. This distinction helps nature avoid confusing DNA and RNA in cellular environments in which untoward things might result from the unwanted behavior if the enzymes that operate on the respective molecules.
While only DNA is double-stranded, RNA is far more adept at forming elaborate three-dimensional structures. This has allowed for three essential forms of RNA to develop in cells.
The Three Types of RNA
RNA comes in three basic types, although additional, very obscure varieties exist as well.
Messenger RNA (mRNA): mRNA molecules contain the coding sequence for proteins. The mRNA molecules vary greatly in length, with eukaryotes (essentially, most living things that are not bacteria) including the largest RNA yet discovered. Many transcripts exceed 100,000 bases (100 kilobases, or kb) in length.
Transfer RNA (tRNA): tRNA is a short (about 75 bases) molecule that transports amino acids and moves them to the growing protein during translation. tRNAs are believed to have a common three-dimensional arrangement that looks like a cloverleaf on X-ray analysis. This is brought about by the binding of complementary bases when a tRNA strand folds back on itself, much like tape sticking to itself when you accidentally bring the sides of a strip of it together.
Ribosomal RNA (rRNA): rRNA molecules comprise 65 to 70 percent of the mass of the organelle called the ribosome, the structure that directly hosts translation, or protein synthesis. Ribosomes are very large by cell standards. Bacterial ribosomes have molecular weights of about 2.5 million, while eukaryotic ribosomes have molecular weights about one and a half times that. (For reference, the molecular weight of carbon is 12; no single element tops 300.)
One eukaryotic ribosome, called 40S, contains one rRNA as well as about 35 different proteins. The 60S ribosome contains three rRNA and about 50 proteins. Ribosomes are thus a mishmash of nucleic acids (rRNA) and the protein products that other nucleic acids (mRNA) carry the code to create.
Until recently, molecular biologists assumed that the rRNA performed a mostly structural role. More recent information, however, indicates that the rRNA in ribosomes acts as an enzyme, while the proteins surrounding it act as scaffolding.
Transcription: How RNA Is Formed
Transcription is the process of synthesizing RNA from a DNA template. Since DNA is double-stranded and RNA is single-stranded, the strands of DNA must be separated before transcription can occur.
Some terminology is useful at this point. A gene, which everyone has heard of but few non-biology experts can formally define, is just a stretch of DNA that contains both a template for RNA synthesis and sequences of nucleotides that allow RNA production to be regulated and controlled from the template region. When the mechanisms for protein synthesis were first described with precision, scientists hypothesized that that each gene corresponded to a single protein product. As convenient as this would be (and as much sense as it makes on the surface), the idea has been proven incorrect. Some genes do not code for proteins at all, and in some animals, "alternate splicing" in which the same gene can be triggered to make different proteins under different conditions, appears to be common.
RNA transcription produces a product that is complementary to the DNA template. This means that it is a mirror image of sorts, and would naturally pair to any sequence identical to the template thanks to the specific base-base pairing rules noted previously. For example, the DNA sequence TACTGGT is complementary to the RNA sequence AUGACCA, since each base in the first sequence can be paired pair to the corresponding base in the second sequence (note that U appears in RNA where T would appear in DNA).
Initiation of transcription is a complex but orderly process. The steps include:
- Transcription factor proteins bind to a promoter "upstream" of the sequence to be transcribed.
- RNA polymerase (the enzyme that assembles new RNA) binds to the promoter-protein complex of the DNA, which is rather like the ignition switch in a car.
- The newly formed RNA polymerase/promoter-protein complex separates the two complementary DNA strands.
- RNA polymerase begins synthesizing RNA, one nucleotide at a time.
Unlike DNA polymerase, RNA polymerase does not need to be "primed" by a second enzyme. Transcription only requires binding of the RNA polymerase to the promoter area.
Translation: RNA on Full Display
The genes in DNA encode protein molecules. These are the "foot soldiers" of the cell, carrying out the duties needed to sustain life. You may think of meat or muscle or a healthful shake when you think of a protein, but most proteins fly under the radar of your everyday life. Enzymes are proteins – molecules that help break down nutrients, build new cell components, assemble nucleic acids (e.g., DNA polymerase) and make copies of DNA during cell division.
"Gene expression" means manufacturing the gene's corresponding protein, if any, and this complicated process has two primary steps. The first is transcription, detailed previously. In translation, newly made mRNA molecules exit the nucleus and migrate to the cytoplasm, where ribosomes are located. (In prokaryotic organisms, ribosomes can attach to mRNA while transcription is still underway.)
Ribosomes consists of two distinct portions: the large subunit and the small subunit. Each subunit is usually separated in the cytoplasm, but they come together on a molecule mRNA. The subunits contain a little of almost everything already mentioned: proteins, rRNA and tRNA. The tRNA molecules are adapter molecules: One end can read the triplet code in the mRNA (for example, UAG or CGC) via complementary base-pairing, and the other end attaches to a specific amino acid. Each triplet code is responsible for one of the approximately 20 amino acids that make up all proteins; some amino acids are coded for by multiple triplets (which is not surprising, since 64 triplets are possible – four bases raised to the third power because each triplet has three bases – and only 20 amino acids are needed). In the ribosome, mRNA and aminoacyl-tRNA complexes (pieces of tRNA shuttling an amino acid) are held very close together, facilitating base-pairing. rRNA catalyzes the attachment of each additional amino acid to the growing chain, which becomes a polypeptide and finally a protein.
The RNA World
As a result of its ability to arrange itself into complex shapes, RNA can act weakly as an enzyme. Because RNA can both store genetic information and catalyze reactions, some scientists have suggested a major role for RNA in the origin of life, called "the RNA World." This hypothesis contends that, far back in Earth's history, RNA molecules played all of the same roles of protein and nucleic acid molecules play today, which would be impossible now but might have been possible in a pre-biotic world. If RNA acted as both an information-storage structure and as the source of the catalytic activity needed for basic metabolic reactions, it may have preceded DNA in its earliest forms (even though it is now made by DNA) and served as a platform for the launching of "organisms" that are truly self-replicating.